No one in Israel is admitting that its pilots carried out a long-range raid against a munitions factory in Sudan, said to be supplying weapons to the Palestinian movement Hamas in the Gaza Strip.

But no one is denying it either. Amos Gilad, a senior defence ministry official, ducked a direct question, praising the capabilities of Israel's air force and calling Sudan "a dangerous terrorist state".

This is one of those episodes where motive, capability and precedent all matter. Sudan's angry accusation that Israel bombed the Yarmouk factory in Khartoum is highly plausible. The attack appears to offer a rare glimpse of a secret war that has been going on for years.

Israel could mount a raid like this using F-16 fighters, flying south along the Red Sea coast, under Saudi and Egyptian radar and with aerial refuelling. It would take about two and a half hours each way. Experts say drones could also be used. The same long-range capability could allow it to strike nuclear facilities in Iran.

Another tantalising glimpse of this clandestine war came in January 2010, when suspected Mossad agents assassinated Mohammed Mabhouh in a Dubai hotel. Mabhouh was described as the link man between Hamas and Iran. The following year a mysterious missile strike on a car near Port Sudan airport killed his replacement. Hamas denied the story while Sudan called the attack a "desperate Israeli attempt" to smear the country's image and scupper its bid to be removed from the US list of state sponsors of terrorism. Sudan has denied allowing weapons-smuggling through its territory.

Detailed evidence of Israel's efforts to block arms shipments to Hamas (and to Hezbollah in Lebanon) surfaced in WikiLeaks documents published by the Guardian. They demonstrated that Sudan was warned by the US in January 2009 not to allow the delivery of unspecified Iranian arms that were expected to be passed to Hamas in Gaza around the time of Israel's Cast Lead offensive, in which 1,400 Palestinians were killed.

Israeli media has reported that the Israeli air force carried out at least two secret operations in Sudan in January and February 2009. The first involved the bombing of a convoy carrying arms through Sudan to Gaza, in which 119 people were killed. And a ship at a Sudanese port was bombed from the air. Sudan accused the US of carrying out these attacks. In June that year Binyamin Netanyahu, Israel's prime minister, told US officials there was "a steady flow of Iranian weapons to Gaza through Sudan or Syria and then by sea".

Only rarely did the US cables show evidence of direct Israeli requests to the US to block arms deliveries. But in one meeting in 2009 a senior US state department official noted: "Most requests to third countries to deny arms transfer overflights are based on Israeli intelligence. Additional information/intelligence from the government of Israel would ensure greater co-operation."